I have noticed there is a Persistent ID when exporting the library to an itunes xml file. What about adding an optional "Unsafe, betatesting but really fast synchronization mode" which would store the persistent ID in the files synchronized and when synchronizing again would:
-Pair files matching the same id
-Check if filenames match, rename if not.
-Check if modified date has changed.
-If yes, check audio stream size in bytes
-If changed copy entire file
-If not, copy only the tags
-If not, check filesize
-If changed copy entire file
-If not, do nothing